Rendering Transparent objects with the Cell Fracture addon?
Take advantage of the node compositor and render layers. If you put the original (non-fractured) object on a separate render layer, you can smooth out the transition. Basically, the idea would be to reduce the opacity of the original object's render layer over the span of a few frames rather than use the hard swap that you currently have. Stretching that transition over more than a couple frames will make the change less apparent.

This can also be done from the VSE, but you'd need to either use separate scene strips or render the animation twice (once with the original object and once with the fractured object).